Transcriptomic and epigenomic analysis of neuronal differentiation models of Kabuki Syndrome Type 1 [RNA-Seq]
RNA-seq (gene expression) · human · 23 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Samples
- 23 samples: 6 conditions, mostly in triplicateGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- Epigenome and transcriptome changes in KMT2D-related Kabuki syndrome Type 1 iPSCs, neuronal progenitors and cortical neuronsPLoS genetics · 2025
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE289159_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1221827 and SRA study SRP563023. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 17 samples.
How we read this: 6 replicated groups read from 23 sample titles; they account for 17 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM8785501 iPSC, Control, rep1 iPSC, Control,
- GSM8785502 iPSC, Control, rep2 iPSC, Control,
- GSM8785503 iPSC, Control, rep3 iPSC, Control,
- GSM8785504 iPSC, Kabuki Syndrome 1, rep1 iPSC, Kabuki Syndrome 1,
- GSM8785505 iPSC, Kabuki Syndrome 1, rep2 iPSC, Kabuki Syndrome 1,
- GSM8785506 iPSC, Kabuki Syndrome 1, rep3 iPSC, Kabuki Syndrome 1,
- GSM8785507 Neuronal progenitor, Control, rep1 Neuronal progenitor, Co…
- GSM8785508 Neuronal progenitor, Control, rep2 Neuronal progenitor, Co…
- GSM8785509 Neuronal progenitor, Control, rep3 Neuronal progenitor, Co…
- GSM8785510 Neuronal progenitor, Kabuki Syndrome 1, rep1 Neuronal progenitor, Ka…
- GSM8785511 Neuronal progenitor, Kabuki Syndrome 1, rep2 Neuronal progenitor, Ka…
- GSM8785512 Neuronal progenitor, Kabuki Syndrome 1, rep3 Neuronal progenitor, Ka…
- GSM8785513 Neuronal progenitor, Control, rep1, validation dataset DS2
- GSM8785514 Neuronal progenitor, Control, rep2, validation dataset DS2
- GSM8785515 Neuronal progenitor, Control, rep3, validation dataset DS2
- GSM8785516 Neuronal progenitor, Kabuki Syndrome 1, rep1, validation dataset DS2
- GSM8785517 Neuronal progenitor, Kabuki Syndrome 1, rep2, validation dataset DS2
- GSM8785518 Neuronal progenitor, Kabuki Syndrome 1, rep3, validation dataset DS2
- GSM8785519 Cortical neuron, Control, rep1 Cortical neuron, Contro…
- GSM8785520 Cortical neuron, Control, rep2 Cortical neuron, Contro…
- GSM8785521 Cortical neuron, Kabuki Syndrome 1, rep1 Cortical neuron, Kabuki…
- GSM8785522 Cortical neuron, Kabuki Syndrome 1, rep2 Cortical neuron, Kabuki…
- GSM8785523 Cortical neuron, Kabuki Syndrome 1, rep3 Cortical neuron, Kabuki…
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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.